Overview
Spatial Point Pattern Analysis is the evaluation of the pattern or distribution, of a set of points on a surface. Examples of location of point include:
events such as crime, traffic accident and disease onset
business services (coffee and fastfood outlets) or facilities such as childcare and eldercare
Data Used
The following datasets were used:
CHILDCARE, a point feature data providing both location and attribute information of childcare centres. It was downloaded from Data.gov.sg and is in geojson format.MP14_SUBZONE_WEB_PL, a polygon feature data providing information of URA 2014 Master Plan Planning Subzone boundary data. It is in ESRI shapefile format. This data set was also downloaded from Data.gov.sg.CostalOutline, a polygon feature data showing the national boundary of Singapore. It is provided by SLA and is in ESRI shapefile format.
Installing and Loading the R packages
sf: used to import, manage and process vector-based geospatial data in R.
spatstat: for point pattern analysis.
raster: reads, writes, manipulates, analyses and model of gridded spatial data.
maptools: provides a set of tools for manipulating geographic data.
tmap: provides functions for plotting cartographic quality static point patterns maps or interactive maps by using leaflet API.
packages = c('maptools', 'sf', 'raster','spatstat', 'tmap','tidyverse' )
for (p in packages){
if(!require(p, character.only = T)){
install.packages(p)
}
library(p,character.only = T)
}
Spatial Data Wrangling
Importing the spatial data
childcare_sf <- st_read("data/child-care-services-geojson.geojson") %>%
st_transform(crs = 3414)
Reading layer `child-care-services-geojson' from data source
`C:\nxinyan\IS415\IS415_blog\_posts\2021-10-26-hands-on-exercise-4\data\child-care-services-geojson.geojson'
using driver `GeoJSON'
Simple feature collection with 1545 features and 2 fields
Geometry type: POINT
Dimension: XYZ
Bounding box: xmin: 103.6824 ymin: 1.248403 xmax: 103.9897 ymax: 1.462134
z_range: zmin: 0 zmax: 0
Geodetic CRS: WGS 84sg_sf <- st_read(dsn = "data", layer="CostalOutline")
Reading layer `CostalOutline' from data source
`C:\nxinyan\IS415\IS415_blog\_posts\2021-10-26-hands-on-exercise-4\data'
using driver `ESRI Shapefile'
Simple feature collection with 60 features and 4 fields
Geometry type: POLYGON
Dimension: XY
Bounding box: xmin: 2663.926 ymin: 16357.98 xmax: 56047.79 ymax: 50244.03
Projected CRS: SVY21mpsz_sf <- st_read(dsn = "data",
layer = "MP14_SUBZONE_WEB_PL")
Reading layer `MP14_SUBZONE_WEB_PL' from data source
`C:\nxinyan\IS415\IS415_blog\_posts\2021-10-26-hands-on-exercise-4\data'
using driver `ESRI Shapefile'
Simple feature collection with 323 features and 15 fields
Geometry type: MULTIPOLYGON
Dimension: XY
Bounding box: xmin: 2667.538 ymin: 15748.72 xmax: 56396.44 ymax: 50256.33
Projected CRS: SVY21DIY: Using the appropriate sf function you learned in Hands-on Exercise 2, retrieve the referencing system information of these geospatial data.
Show code
st_crs(childcare_sf)
Coordinate Reference System:
User input: EPSG:3414
wkt:
PROJCRS["SVY21 / Singapore TM",
BASEGEOGCRS["SVY21",
DATUM["SVY21",
ELLIPSOID["WGS 84",6378137,298.257223563,
LENGTHUNIT["metre",1]]],
PRIMEM["Greenwich",0,
ANGLEUNIT["degree",0.0174532925199433]],
ID["EPSG",4757]],
CONVERSION["Singapore Transverse Mercator",
METHOD["Transverse Mercator",
ID["EPSG",9807]],
PARAMETER["Latitude of natural origin",1.36666666666667,
ANGLEUNIT["degree",0.0174532925199433],
ID["EPSG",8801]],
PARAMETER["Longitude of natural origin",103.833333333333,
ANGLEUNIT["degree",0.0174532925199433],
ID["EPSG",8802]],
PARAMETER["Scale factor at natural origin",1,
SCALEUNIT["unity",1],
ID["EPSG",8805]],
PARAMETER["False easting",28001.642,
LENGTHUNIT["metre",1],
ID["EPSG",8806]],
PARAMETER["False northing",38744.572,
LENGTHUNIT["metre",1],
ID["EPSG",8807]]],
CS[Cartesian,2],
AXIS["northing (N)",north,
ORDER[1],
LENGTHUNIT["metre",1]],
AXIS["easting (E)",east,
ORDER[2],
LENGTHUNIT["metre",1]],
USAGE[
SCOPE["Cadastre, engineering survey, topographic mapping."],
AREA["Singapore - onshore and offshore."],
BBOX[1.13,103.59,1.47,104.07]],
ID["EPSG",3414]]Show code
st_crs(mpsz_sf)
Coordinate Reference System:
User input: SVY21
wkt:
PROJCRS["SVY21",
BASEGEOGCRS["SVY21[WGS84]",
DATUM["World Geodetic System 1984",
ELLIPSOID["WGS 84",6378137,298.257223563,
LENGTHUNIT["metre",1]],
ID["EPSG",6326]],
PRIMEM["Greenwich",0,
ANGLEUNIT["Degree",0.0174532925199433]]],
CONVERSION["unnamed",
METHOD["Transverse Mercator",
ID["EPSG",9807]],
PARAMETER["Latitude of natural origin",1.36666666666667,
ANGLEUNIT["Degree",0.0174532925199433],
ID["EPSG",8801]],
PARAMETER["Longitude of natural origin",103.833333333333,
ANGLEUNIT["Degree",0.0174532925199433],
ID["EPSG",8802]],
PARAMETER["Scale factor at natural origin",1,
SCALEUNIT["unity",1],
ID["EPSG",8805]],
PARAMETER["False easting",28001.642,
LENGTHUNIT["metre",1],
ID["EPSG",8806]],
PARAMETER["False northing",38744.572,
LENGTHUNIT["metre",1],
ID["EPSG",8807]]],
CS[Cartesian,2],
AXIS["(E)",east,
ORDER[1],
LENGTHUNIT["metre",1,
ID["EPSG",9001]]],
AXIS["(N)",north,
ORDER[2],
LENGTHUNIT["metre",1,
ID["EPSG",9001]]]]Show code
st_crs(sg_sf)
Coordinate Reference System:
User input: SVY21
wkt:
PROJCRS["SVY21",
BASEGEOGCRS["SVY21[WGS84]",
DATUM["World Geodetic System 1984",
ELLIPSOID["WGS 84",6378137,298.257223563,
LENGTHUNIT["metre",1]],
ID["EPSG",6326]],
PRIMEM["Greenwich",0,
ANGLEUNIT["Degree",0.0174532925199433]]],
CONVERSION["unnamed",
METHOD["Transverse Mercator",
ID["EPSG",9807]],
PARAMETER["Latitude of natural origin",1.36666666666667,
ANGLEUNIT["Degree",0.0174532925199433],
ID["EPSG",8801]],
PARAMETER["Longitude of natural origin",103.833333333333,
ANGLEUNIT["Degree",0.0174532925199433],
ID["EPSG",8802]],
PARAMETER["Scale factor at natural origin",1,
SCALEUNIT["unity",1],
ID["EPSG",8805]],
PARAMETER["False easting",28001.642,
LENGTHUNIT["metre",1],
ID["EPSG",8806]],
PARAMETER["False northing",38744.572,
LENGTHUNIT["metre",1],
ID["EPSG",8807]]],
CS[Cartesian,2],
AXIS["(E)",east,
ORDER[1],
LENGTHUNIT["metre",1,
ID["EPSG",9001]]],
AXIS["(N)",north,
ORDER[2],
LENGTHUNIT["metre",1,
ID["EPSG",9001]]]]DIY: Using the method you learned in Lesson 2, assign the correct crs to mpsz_sf and sg_sf simple feature data frames.
mpsz3414_sf <- st_transform(mpsz_sf,
crs = 3414)
sg3414_sf <- st_transform(sg_sf,
crs = 3414)
st_crs(mpsz3414_sf)
Coordinate Reference System:
User input: EPSG:3414
wkt:
PROJCRS["SVY21 / Singapore TM",
BASEGEOGCRS["SVY21",
DATUM["SVY21",
ELLIPSOID["WGS 84",6378137,298.257223563,
LENGTHUNIT["metre",1]]],
PRIMEM["Greenwich",0,
ANGLEUNIT["degree",0.0174532925199433]],
ID["EPSG",4757]],
CONVERSION["Singapore Transverse Mercator",
METHOD["Transverse Mercator",
ID["EPSG",9807]],
PARAMETER["Latitude of natural origin",1.36666666666667,
ANGLEUNIT["degree",0.0174532925199433],
ID["EPSG",8801]],
PARAMETER["Longitude of natural origin",103.833333333333,
ANGLEUNIT["degree",0.0174532925199433],
ID["EPSG",8802]],
PARAMETER["Scale factor at natural origin",1,
SCALEUNIT["unity",1],
ID["EPSG",8805]],
PARAMETER["False easting",28001.642,
LENGTHUNIT["metre",1],
ID["EPSG",8806]],
PARAMETER["False northing",38744.572,
LENGTHUNIT["metre",1],
ID["EPSG",8807]]],
CS[Cartesian,2],
AXIS["northing (N)",north,
ORDER[1],
LENGTHUNIT["metre",1]],
AXIS["easting (E)",east,
ORDER[2],
LENGTHUNIT["metre",1]],
USAGE[
SCOPE["Cadastre, engineering survey, topographic mapping."],
AREA["Singapore - onshore and offshore."],
BBOX[1.13,103.59,1.47,104.07]],
ID["EPSG",3414]]st_crs(sg3414_sf)
Coordinate Reference System:
User input: EPSG:3414
wkt:
PROJCRS["SVY21 / Singapore TM",
BASEGEOGCRS["SVY21",
DATUM["SVY21",
ELLIPSOID["WGS 84",6378137,298.257223563,
LENGTHUNIT["metre",1]]],
PRIMEM["Greenwich",0,
ANGLEUNIT["degree",0.0174532925199433]],
ID["EPSG",4757]],
CONVERSION["Singapore Transverse Mercator",
METHOD["Transverse Mercator",
ID["EPSG",9807]],
PARAMETER["Latitude of natural origin",1.36666666666667,
ANGLEUNIT["degree",0.0174532925199433],
ID["EPSG",8801]],
PARAMETER["Longitude of natural origin",103.833333333333,
ANGLEUNIT["degree",0.0174532925199433],
ID["EPSG",8802]],
PARAMETER["Scale factor at natural origin",1,
SCALEUNIT["unity",1],
ID["EPSG",8805]],
PARAMETER["False easting",28001.642,
LENGTHUNIT["metre",1],
ID["EPSG",8806]],
PARAMETER["False northing",38744.572,
LENGTHUNIT["metre",1],
ID["EPSG",8807]]],
CS[Cartesian,2],
AXIS["northing (N)",north,
ORDER[1],
LENGTHUNIT["metre",1]],
AXIS["easting (E)",east,
ORDER[2],
LENGTHUNIT["metre",1]],
USAGE[
SCOPE["Cadastre, engineering survey, topographic mapping."],
AREA["Singapore - onshore and offshore."],
BBOX[1.13,103.59,1.47,104.07]],
ID["EPSG",3414]]st_crs(childcare_sf)
Coordinate Reference System:
User input: EPSG:3414
wkt:
PROJCRS["SVY21 / Singapore TM",
BASEGEOGCRS["SVY21",
DATUM["SVY21",
ELLIPSOID["WGS 84",6378137,298.257223563,
LENGTHUNIT["metre",1]]],
PRIMEM["Greenwich",0,
ANGLEUNIT["degree",0.0174532925199433]],
ID["EPSG",4757]],
CONVERSION["Singapore Transverse Mercator",
METHOD["Transverse Mercator",
ID["EPSG",9807]],
PARAMETER["Latitude of natural origin",1.36666666666667,
ANGLEUNIT["degree",0.0174532925199433],
ID["EPSG",8801]],
PARAMETER["Longitude of natural origin",103.833333333333,
ANGLEUNIT["degree",0.0174532925199433],
ID["EPSG",8802]],
PARAMETER["Scale factor at natural origin",1,
SCALEUNIT["unity",1],
ID["EPSG",8805]],
PARAMETER["False easting",28001.642,
LENGTHUNIT["metre",1],
ID["EPSG",8806]],
PARAMETER["False northing",38744.572,
LENGTHUNIT["metre",1],
ID["EPSG",8807]]],
CS[Cartesian,2],
AXIS["northing (N)",north,
ORDER[1],
LENGTHUNIT["metre",1]],
AXIS["easting (E)",east,
ORDER[2],
LENGTHUNIT["metre",1]],
USAGE[
SCOPE["Cadastre, engineering survey, topographic mapping."],
AREA["Singapore - onshore and offshore."],
BBOX[1.13,103.59,1.47,104.07]],
ID["EPSG",3414]]Mapping the geospatial data sets
DIY: Using the mapping methods you learned in Hands-on Exercise 3, prepare a map as shown below.
tm_shape(sg3414_sf) +
tm_polygons() +
tm_shape(mpsz3414_sf) +
tm_polygons() +
tm_shape(childcare_sf)+
tm_dots()
tmap_mode('view')
tm_shape(childcare_sf)+
tm_dots()
tmap_mode('plot')
Geospatial Data Wrangling
Converting sf data frames to sp’s Spatial* class
childcare <- as_Spatial(childcare_sf)
mpsz <- as_Spatial(mpsz_sf)
sg <- as_Spatial(sg_sf)
DIY: Using appropriate function, display the information of these three Spatial classes as shown below.
childcare
class : SpatialPointsDataFrame
features : 1545
extent : 11203.01, 45404.24, 25667.6, 49300.88 (xmin, xmax, ymin, ymax)
crs : +proj=tmerc +lat_0=1.36666666666667 +lon_0=103.833333333333 +k=1 +x_0=28001.642 +y_0=38744.572 +ellps=WGS84 +towgs84=0,0,0,0,0,0,0 +units=m +no_defs
variables : 2
names : Name, Description
min values : kml_1, <center><table><tr><th colspan='2' align='center'><em>Attributes</em></th></tr><tr bgcolor="#E3E3F3"> <th>ADDRESSBLOCKHOUSENUMBER</th> <td></td> </tr><tr bgcolor=""> <th>ADDRESSBUILDINGNAME</th> <td></td> </tr><tr bgcolor="#E3E3F3"> <th>ADDRESSPOSTALCODE</th> <td>018989</td> </tr><tr bgcolor=""> <th>ADDRESSSTREETNAME</th> <td>1, MARINA BOULEVARD, #B1 - 01, ONE MARINA BOULEVARD, SINGAPORE 018989</td> </tr><tr bgcolor="#E3E3F3"> <th>ADDRESSTYPE</th> <td></td> </tr><tr bgcolor=""> <th>DESCRIPTION</th> <td></td> </tr><tr bgcolor="#E3E3F3"> <th>HYPERLINK</th> <td></td> </tr><tr bgcolor=""> <th>LANDXADDRESSPOINT</th> <td>0</td> </tr><tr bgcolor="#E3E3F3"> <th>LANDYADDRESSPOINT</th> <td>0</td> </tr><tr bgcolor=""> <th>NAME</th> <td>THE LITTLE SKOOL-HOUSE INTERNATIONAL PTE. LTD.</td> </tr><tr bgcolor="#E3E3F3"> <th>PHOTOURL</th> <td></td> </tr><tr bgcolor=""> <th>ADDRESSFLOORNUMBER</th> <td></td> </tr><tr bgcolor="#E3E3F3"> <th>INC_CRC</th> <td>08F73931F4A691F4</td> </tr><tr bgcolor=""> <th>FMEL_UPD_D</th> <td>20200826094036</td> </tr><tr bgcolor="#E3E3F3"> <th>ADDRESSUNITNUMBER</th> <td></td> </tr></table></center>
max values : kml_999, <center><table><tr><th colspan='2' align='center'><em>Attributes</em></th></tr><tr bgcolor="#E3E3F3"> <th>ADDRESSBLOCKHOUSENUMBER</th> <td></td> </tr><tr bgcolor=""> <th>ADDRESSBUILDINGNAME</th> <td></td> </tr><tr bgcolor="#E3E3F3"> <th>ADDRESSPOSTALCODE</th> <td>829646</td> </tr><tr bgcolor=""> <th>ADDRESSSTREETNAME</th> <td>200, PONGGOL SEVENTEENTH AVENUE, SINGAPORE 829646</td> </tr><tr bgcolor="#E3E3F3"> <th>ADDRESSTYPE</th> <td></td> </tr><tr bgcolor=""> <th>DESCRIPTION</th> <td>Child Care Services</td> </tr><tr bgcolor="#E3E3F3"> <th>HYPERLINK</th> <td></td> </tr><tr bgcolor=""> <th>LANDXADDRESSPOINT</th> <td>0</td> </tr><tr bgcolor="#E3E3F3"> <th>LANDYADDRESSPOINT</th> <td>0</td> </tr><tr bgcolor=""> <th>NAME</th> <td>RAFFLES KIDZ @ PUNGGOL PTE LTD</td> </tr><tr bgcolor="#E3E3F3"> <th>PHOTOURL</th> <td></td> </tr><tr bgcolor=""> <th>ADDRESSFLOORNUMBER</th> <td></td> </tr><tr bgcolor="#E3E3F3"> <th>INC_CRC</th> <td>379D017BF244B0FA</td> </tr><tr bgcolor=""> <th>FMEL_UPD_D</th> <td>20200826094036</td> </tr><tr bgcolor="#E3E3F3"> <th>ADDRESSUNITNUMBER</th> <td></td> </tr></table></center> mpsz
class : SpatialPolygonsDataFrame
features : 323
extent : 2667.538, 56396.44, 15748.72, 50256.33 (xmin, xmax, ymin, ymax)
crs : +proj=tmerc +lat_0=1.36666666666667 +lon_0=103.833333333333 +k=1 +x_0=28001.642 +y_0=38744.572 +datum=WGS84 +units=m +no_defs
variables : 15
names : OBJECTID, SUBZONE_NO, SUBZONE_N, SUBZONE_C, CA_IND, PLN_AREA_N, PLN_AREA_C, REGION_N, REGION_C, INC_CRC, FMEL_UPD_D, X_ADDR, Y_ADDR, SHAPE_Leng, SHAPE_Area
min values : 1, 1, ADMIRALTY, AMSZ01, N, ANG MO KIO, AM, CENTRAL REGION, CR, 00F5E30B5C9B7AD8, 16409, 5092.8949, 19579.069, 871.554887798, 39437.9352703
max values : 323, 17, YUNNAN, YSSZ09, Y, YISHUN, YS, WEST REGION, WR, FFCCF172717C2EAF, 16409, 50424.7923, 49552.7904, 68083.9364708, 69748298.792 sg
class : SpatialPolygonsDataFrame
features : 60
extent : 2663.926, 56047.79, 16357.98, 50244.03 (xmin, xmax, ymin, ymax)
crs : +proj=tmerc +lat_0=1.36666666666667 +lon_0=103.833333333333 +k=1 +x_0=28001.642 +y_0=38744.572 +datum=WGS84 +units=m +no_defs
variables : 4
names : GDO_GID, MSLINK, MAPID, COSTAL_NAM
min values : 1, 1, 0, ISLAND LINK
max values : 60, 67, 0, SINGAPORE - MAIN ISLAND Converting the Spatial* class into generic sp format
spatstat requires the analytical data in ppp object form. There is no direct way to convert a Spatial* classes into ppp object. We need to convert the Spatial classes* into Spatial object first.
childcare_sp <- as(childcare, "SpatialPoints")
sg_sp <- as(sg, "SpatialPolygons")
childcare_sp
class : SpatialPoints
features : 1545
extent : 11203.01, 45404.24, 25667.6, 49300.88 (xmin, xmax, ymin, ymax)
crs : +proj=tmerc +lat_0=1.36666666666667 +lon_0=103.833333333333 +k=1 +x_0=28001.642 +y_0=38744.572 +ellps=WGS84 +towgs84=0,0,0,0,0,0,0 +units=m +no_defs sg_sp
class : SpatialPolygons
features : 60
extent : 2663.926, 56047.79, 16357.98, 50244.03 (xmin, xmax, ymin, ymax)
crs : +proj=tmerc +lat_0=1.36666666666667 +lon_0=103.833333333333 +k=1 +x_0=28001.642 +y_0=38744.572 +datum=WGS84 +units=m +no_defs Converting the generic sp format into spatstat’s ppp format
Now, we will use as.ppp() function of spatstat to convert the spatial data into spatstat’s ppp object format.
childcare_ppp <- as(childcare_sp, "ppp")
childcare_ppp
Planar point pattern: 1545 points
window: rectangle = [11203.01, 45404.24] x [25667.6, 49300.88] unitsplot(childcare_ppp)
summary(childcare_ppp)
Planar point pattern: 1545 points
Average intensity 1.91145e-06 points per square unit
*Pattern contains duplicated points*
Coordinates are given to 3 decimal places
i.e. rounded to the nearest multiple of 0.001 units
Window: rectangle = [11203.01, 45404.24] x [25667.6, 49300.88] units
(34200 x 23630 units)
Window area = 808287000 square unitsNotice the warning message about duplicates. In spatial point patterns analysis an issue of significant is the presence of duplicates. The statistical methodology used for spatial point patterns processes is based largely on the assumption that process are simple, that is, that the points cannot be coincident.
Handling duplicated points
Checking for duplicate
any(duplicated(childcare_ppp))
[1] TRUECount the number of co-indicence point
multiplicity(childcare_ppp)
To know how many locations have more than one point event
sum(multiplicity(childcare_ppp) > 1)
[1] 128tmap_mode('view')
tm_shape(childcare) +
tm_dots(alpha=0.4,
size=0.05)
tmap_mode('plot')
Solving the duplicate problem
There are 3 ways to solve this:
Delete the duplicates, however useful point events will be lost.
Jittering, add a small perturbation to the duplicate points so that they do not occupy the exact same space.
Make each point “unique” and then attach the duplicates of the points to the patterns as marks, as attributes of the points. Then you would need analytical techniques that take into account these marks.
Implements the jittering approach below:
childcare_ppp_jit <- rjitter(childcare_ppp,
retry=TRUE,
nsim=1,
drop=TRUE)
DIY: Using the method you learned in previous section, check if any dusplicated point in this geospatial data.
any(duplicated(childcare_ppp_jit))
[1] FALSECreating owin object
When analysing spatial point patterns, it is a good practice to confine the analysis with a geographical area like Singapore boundary.
sg_owin <- as(sg_sp, "owin")
plot(sg_owin)
summary(sg_owin)
Window: polygonal boundary
60 separate polygons (no holes)
vertices area relative.area
polygon 1 38 1.56140e+04 2.09e-05
polygon 2 735 4.69093e+06 6.27e-03
polygon 3 49 1.66986e+04 2.23e-05
polygon 4 76 3.12332e+05 4.17e-04
polygon 5 5141 6.36179e+08 8.50e-01
polygon 6 42 5.58317e+04 7.46e-05
polygon 7 67 1.31354e+06 1.75e-03
polygon 8 15 4.46420e+03 5.96e-06
polygon 9 14 5.46674e+03 7.30e-06
polygon 10 37 5.26194e+03 7.03e-06
polygon 11 53 3.44003e+04 4.59e-05
polygon 12 74 5.82234e+04 7.78e-05
polygon 13 69 5.63134e+04 7.52e-05
polygon 14 143 1.45139e+05 1.94e-04
polygon 15 165 3.38736e+05 4.52e-04
polygon 16 130 9.40465e+04 1.26e-04
polygon 17 19 1.80977e+03 2.42e-06
polygon 18 16 2.01046e+03 2.69e-06
polygon 19 93 4.30642e+05 5.75e-04
polygon 20 90 4.15092e+05 5.54e-04
polygon 21 721 1.92795e+06 2.57e-03
polygon 22 330 1.11896e+06 1.49e-03
polygon 23 115 9.28394e+05 1.24e-03
polygon 24 37 1.01705e+04 1.36e-05
polygon 25 25 1.66227e+04 2.22e-05
polygon 26 10 2.14507e+03 2.86e-06
polygon 27 190 2.02489e+05 2.70e-04
polygon 28 175 9.25904e+05 1.24e-03
polygon 29 1993 9.99217e+06 1.33e-02
polygon 30 38 2.42492e+04 3.24e-05
polygon 31 24 6.35239e+03 8.48e-06
polygon 32 53 6.35791e+05 8.49e-04
polygon 33 41 1.60161e+04 2.14e-05
polygon 34 22 2.54368e+03 3.40e-06
polygon 35 30 1.08382e+04 1.45e-05
polygon 36 327 2.16921e+06 2.90e-03
polygon 37 111 6.62927e+05 8.85e-04
polygon 38 90 1.15991e+05 1.55e-04
polygon 39 98 6.26829e+04 8.37e-05
polygon 40 415 3.25384e+06 4.35e-03
polygon 41 222 1.51142e+06 2.02e-03
polygon 42 107 6.33039e+05 8.45e-04
polygon 43 7 2.48299e+03 3.32e-06
polygon 44 17 3.28303e+04 4.38e-05
polygon 45 26 8.34758e+03 1.11e-05
polygon 46 177 4.67446e+05 6.24e-04
polygon 47 16 3.19460e+03 4.27e-06
polygon 48 15 4.87296e+03 6.51e-06
polygon 49 66 1.61841e+04 2.16e-05
polygon 50 149 5.63430e+06 7.53e-03
polygon 51 609 2.62570e+07 3.51e-02
polygon 52 8 7.82256e+03 1.04e-05
polygon 53 976 2.33447e+07 3.12e-02
polygon 54 55 8.25379e+04 1.10e-04
polygon 55 976 2.33447e+07 3.12e-02
polygon 56 61 3.33449e+05 4.45e-04
polygon 57 6 1.68410e+04 2.25e-05
polygon 58 4 9.45963e+03 1.26e-05
polygon 59 46 6.99702e+05 9.35e-04
polygon 60 13 7.00873e+04 9.36e-05
enclosing rectangle: [2663.93, 56047.79] x [16357.98, 50244.03] units
(53380 x 33890 units)
Window area = 748741000 square units
Fraction of frame area: 0.414Combining point events object and owin object
Extract childcare events that are located within Singapore
childcareSG_ppp = childcare_ppp[sg_owin]
summary(childcareSG_ppp)
Planar point pattern: 1545 points
Average intensity 2.063463e-06 points per square unit
*Pattern contains duplicated points*
Coordinates are given to 3 decimal places
i.e. rounded to the nearest multiple of 0.001 units
Window: polygonal boundary
60 separate polygons (no holes)
vertices area relative.area
polygon 1 38 1.56140e+04 2.09e-05
polygon 2 735 4.69093e+06 6.27e-03
polygon 3 49 1.66986e+04 2.23e-05
polygon 4 76 3.12332e+05 4.17e-04
polygon 5 5141 6.36179e+08 8.50e-01
polygon 6 42 5.58317e+04 7.46e-05
polygon 7 67 1.31354e+06 1.75e-03
polygon 8 15 4.46420e+03 5.96e-06
polygon 9 14 5.46674e+03 7.30e-06
polygon 10 37 5.26194e+03 7.03e-06
polygon 11 53 3.44003e+04 4.59e-05
polygon 12 74 5.82234e+04 7.78e-05
polygon 13 69 5.63134e+04 7.52e-05
polygon 14 143 1.45139e+05 1.94e-04
polygon 15 165 3.38736e+05 4.52e-04
polygon 16 130 9.40465e+04 1.26e-04
polygon 17 19 1.80977e+03 2.42e-06
polygon 18 16 2.01046e+03 2.69e-06
polygon 19 93 4.30642e+05 5.75e-04
polygon 20 90 4.15092e+05 5.54e-04
polygon 21 721 1.92795e+06 2.57e-03
polygon 22 330 1.11896e+06 1.49e-03
polygon 23 115 9.28394e+05 1.24e-03
polygon 24 37 1.01705e+04 1.36e-05
polygon 25 25 1.66227e+04 2.22e-05
polygon 26 10 2.14507e+03 2.86e-06
polygon 27 190 2.02489e+05 2.70e-04
polygon 28 175 9.25904e+05 1.24e-03
polygon 29 1993 9.99217e+06 1.33e-02
polygon 30 38 2.42492e+04 3.24e-05
polygon 31 24 6.35239e+03 8.48e-06
polygon 32 53 6.35791e+05 8.49e-04
polygon 33 41 1.60161e+04 2.14e-05
polygon 34 22 2.54368e+03 3.40e-06
polygon 35 30 1.08382e+04 1.45e-05
polygon 36 327 2.16921e+06 2.90e-03
polygon 37 111 6.62927e+05 8.85e-04
polygon 38 90 1.15991e+05 1.55e-04
polygon 39 98 6.26829e+04 8.37e-05
polygon 40 415 3.25384e+06 4.35e-03
polygon 41 222 1.51142e+06 2.02e-03
polygon 42 107 6.33039e+05 8.45e-04
polygon 43 7 2.48299e+03 3.32e-06
polygon 44 17 3.28303e+04 4.38e-05
polygon 45 26 8.34758e+03 1.11e-05
polygon 46 177 4.67446e+05 6.24e-04
polygon 47 16 3.19460e+03 4.27e-06
polygon 48 15 4.87296e+03 6.51e-06
polygon 49 66 1.61841e+04 2.16e-05
polygon 50 149 5.63430e+06 7.53e-03
polygon 51 609 2.62570e+07 3.51e-02
polygon 52 8 7.82256e+03 1.04e-05
polygon 53 976 2.33447e+07 3.12e-02
polygon 54 55 8.25379e+04 1.10e-04
polygon 55 976 2.33447e+07 3.12e-02
polygon 56 61 3.33449e+05 4.45e-04
polygon 57 6 1.68410e+04 2.25e-05
polygon 58 4 9.45963e+03 1.26e-05
polygon 59 46 6.99702e+05 9.35e-04
polygon 60 13 7.00873e+04 9.36e-05
enclosing rectangle: [2663.93, 56047.79] x [16357.98, 50244.03] units
(53380 x 33890 units)
Window area = 748741000 square units
Fraction of frame area: 0.414DIY: Using the method you learned in previous exercise, plot the newly derived childcareSG_ppp as shown below.
plot(childcareSG_ppp)
First-order Spatial Point Patterns Analysis
Using spatstat package, I learnt how to perform first-order spatial point patterns analysis by:
deriving kernel density estimation (KDE) layer for visualising and exploring the intensity of point processes
performing Confirmatory Spatial Point Patterns Analysis by using Nearest Neighbour statistics.
Kernel Density Estimation
Computing kernel density estimation using automatic bandwidth selection method
kde_childcareSG_bw <- density(childcareSG_ppp,
sigma=bw.diggle,
edge=TRUE,
kernel="gaussian")
plot(kde_childcareSG_bw)
Retrieve the bandwidth used to compute the kde layer:
bw <- bw.diggle(childcareSG_ppp)
bw
sigma
298.4095 Rescalling KDE values
rescale() is used to covert the unit of measurement from meter to kilometer
childcareSG_ppp.km <- rescale(childcareSG_ppp, 1000, "km")
kde_childcareSG.bw <- density(childcareSG_ppp.km, sigma=bw.diggle, edge=TRUE, kernel="gaussian")
plot(kde_childcareSG.bw)
Notice that the data value in the legend has changed!
Working with different automatic badwidth methods
Beside bw.diggle(), there are three other spatstat functions can be used to determine the bandwidth, they are: bw.CvL(), bw.scott(), and bw.ppl().
bw.CvL(childcareSG_ppp.km)
sigma
4.543278 bw.scott(childcareSG_ppp.km)
sigma.x sigma.y
2.224898 1.450966 bw.ppl(childcareSG_ppp.km)
sigma
0.3897114 bw.diggle(childcareSG_ppp.km)
sigma
0.2984095 bw.ppl() algorithm because in ther experience it tends to produce the more appropriate values when the pattern consists predominantly of tight clusters. But they also insist that if the purpose of once study is to detect a single tight cluster in the midst of random noise then the bw.diggle() method seems to work best.
Compare the output of using bw.diggle and bw.ppl methods
kde_childcareSG.ppl <- density(childcareSG_ppp.km,
sigma=bw.ppl,
edge=TRUE,
kernel="gaussian")
par(mfrow=c(1,2))
plot(kde_childcareSG.bw, main = "bw.diggle")
plot(kde_childcareSG.ppl, main = "bw.ppl")
Working with different kernel methods
By default, the kernel method used in density.ppp() is gaussian. But there are three other options, namely: Epanechnikov, Quartic and Dics.
par(mfrow=c(2,2))
plot(density(childcareSG_ppp.km,
sigma=bw.ppl,
edge=TRUE,
kernel="gaussian"),
main="Gaussian")
plot(density(childcareSG_ppp.km,
sigma=bw.ppl,
edge=TRUE,
kernel="epanechnikov"),
main="Epanechnikov")
plot(density(childcareSG_ppp.km,
sigma=bw.ppl,
edge=TRUE,
kernel="quartic"),
main="Quartic")
plot(density(childcareSG_ppp.km,
sigma=bw.ppl,
edge=TRUE,
kernel="disc"),
main="Disc")
Fixed and Adaptive KDE
COMPUTING KDE BY USING FIXED BANDWIDTH
Compute a KDE layer by defining a bandwidth of 600 meter. The sigma value used is 0.6 in the code chunk below.This is because the unit of measurement of childcareSG_ppp.km object is in kilometer, hence the 600m is 0.6km.
kde_childcareSG_600 <- density(childcareSG_ppp.km, sigma=0.6, edge=TRUE, kernel="gaussian")
plot(kde_childcareSG_600)
COMPUTING KDE BY USING ADAPTIVE BANDWIDTH
Fixed bandwidth method is very sensitive to highly skew distribution of spatial point patterns over geographical units for example urban versus rural. To overcome this problem, adaptive bandwidth is used.
kde_childcareSG_adaptive <- adaptive.density(childcareSG_ppp.km, method="kernel")
plot(kde_childcareSG_adaptive)
Compare fixed and adaptive kernel density estimation outputs
par(mfrow=c(1,2))
plot(kde_childcareSG.bw, main = "Fixed bandwidth")
plot(kde_childcareSG_adaptive, main = "Adaptive bandwidth")
Converting KDE output into grid object
For mapping purpose, it is converted even though results are the same.
gridded_kde_childcareSG_bw <- as.SpatialGridDataFrame.im(kde_childcareSG.bw)
spplot(gridded_kde_childcareSG_bw)
CONVERTING GRIDDED OUTPUT INTO RASTER
Next, we will convert the gridded kernal density objects into RasterLayer object by using raster() of raster package
kde_childcareSG_bw_raster <- raster(gridded_kde_childcareSG_bw)
Look at the properties of kde_childcareSG_bw_raster RasterLayer.
kde_childcareSG_bw_raster
class : RasterLayer
dimensions : 128, 128, 16384 (nrow, ncol, ncell)
resolution : 0.4170614, 0.2647348 (x, y)
extent : 2.663926, 56.04779, 16.35798, 50.24403 (xmin, xmax, ymin, ymax)
crs : NA
source : memory
names : v
values : -8.476185e-15, 28.51831 (min, max)Notice that the crs property is NA.
ASSIGNING PROJECTION SYSTEMS
projection(kde_childcareSG_bw_raster) <- CRS("+init=EPSG:3414")
kde_childcareSG_bw_raster
class : RasterLayer
dimensions : 128, 128, 16384 (nrow, ncol, ncell)
resolution : 0.4170614, 0.2647348 (x, y)
extent : 2.663926, 56.04779, 16.35798, 50.24403 (xmin, xmax, ymin, ymax)
crs : +proj=tmerc +lat_0=1.36666666666667 +lon_0=103.833333333333 +k=1 +x_0=28001.642 +y_0=38744.572 +ellps=WGS84 +units=m +no_defs
source : memory
names : v
values : -8.476185e-15, 28.51831 (min, max)Notice that the crs property is completed.
Visualising the output in tmap
Finally, we will display the raster in cartographic quality map using tmap package.
tm_shape(kde_childcareSG_bw_raster) +
tm_raster("v") +
tm_layout(legend.position = c("right", "bottom"), frame = FALSE)
Notice that the raster values are encoded explicitly onto the raster pixel using the values in “v”" field.
Comparing Spatial Point Patterns using KDE
In this section, you will learn how to compare KDE of childcare at Ponggol, Tampines, Chua Chu Kang and Jurong West planning areas.
Extracting Study Area
pg = mpsz[mpsz@data$PLN_AREA_N == "PUNGGOL",]
tm = mpsz[mpsz@data$PLN_AREA_N == "TAMPINES",]
ck = mpsz[mpsz@data$PLN_AREA_N == "CHOA CHU KANG",]
jw = mpsz[mpsz@data$PLN_AREA_N == "JURONG WEST",]
Plotting target planning areas
par(mfrow=c(2,2))
plot(pg, main = "Ponggol")
plot(tm, main = "Tampines")
plot(ck, main = "Choa Chu Kang")
plot(jw, main = "Jurong West")
CONVERTING THE SPATIAL POINT DATA FRAME INTO GENERIC SP FORMAT
Convert the SpatialPolygonsDataFrame layers into generic spatialpolygons layers
pg_sp = as(pg, "SpatialPolygons")
tm_sp = as(tm, "SpatialPolygons")
ck_sp = as(ck, "SpatialPolygons")
jw_sp = as(jw, "SpatialPolygons")
CREATING OWIN OBJECT
Now, we will convert these SpatialPolygons objects into owin objects that is required by spatstat.
pg_owin = as(pg_sp, "owin")
tm_owin = as(tm_sp, "owin")
ck_owin = as(ck_sp, "owin")
jw_owin = as(jw_sp, "owin")
COMBINING CHILDCARE POINTS AND THE STUDY AREA
By using the code chunk below, we are able to extract childcare that is within the specific region to do our analysis later on.
childcare_pg_ppp = childcare_ppp_jit[pg_owin]
childcare_tm_ppp = childcare_ppp_jit[tm_owin]
childcare_ck_ppp = childcare_ppp_jit[ck_owin]
childcare_jw_ppp = childcare_ppp_jit[jw_owin]
Next, rescale() function is used to trasnform the unit of measurement from metre to kilometre.
childcare_pg_ppp.km = rescale(childcare_pg_ppp, 1000, "km")
childcare_tm_ppp.km = rescale(childcare_tm_ppp, 1000, "km")
childcare_ck_ppp.km = rescale(childcare_ck_ppp, 1000, "km")
childcare_jw_ppp.km = rescale(childcare_jw_ppp, 1000, "km")
Plot the four study areas and the locations of the childcare centres.
par(mfrow=c(2,2))
plot(childcare_pg_ppp.km, main="Punggol")
plot(childcare_tm_ppp.km, main="Tampines")
plot(childcare_ck_ppp.km, main="Choa Chu Kang")
plot(childcare_jw_ppp.km, main="Jurong West")
